Contacts of the strand formed by residues 138 - 145 (chain B) in PDB entry 2VRF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MET 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ARG 4.0 0.7 - - - -
138A MET* 4.1 10.1 - - + -
139A PRO* 3.4 25.1 - - + -
141A LEU* 5.0 6.7 - - + -
197A ILE* 4.5 17.3 - - - -
199A GLU* 6.6 0.2 - - - -
131B LYS* 4.5 11.9 - - + -
132B GLY* 3.9 22.7 - - - +
133B GLY* 3.1 26.3 + - - +
134B ARG* 3.7 2.3 + - - +
136B ASN* 3.1 21.0 - - - +
137B ARG* 1.3 75.7 - - - +
139B PRO* 1.3 69.8 - - + +
141B LEU* 3.4 32.3 - - + -
172B ARG 5.5 1.7 - - - +
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Residues in contact with PRO 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ASN 3.8 17.5 - - - +
137A ARG* 3.5 21.5 - - + +
138A MET* 3.7 15.9 - - - -
132B GLY* 3.3 15.1 - - - -
133B GLY 3.8 1.1 - - - -
138B MET* 1.3 90.7 - - + +
140B ILE* 1.3 64.1 + - - +
141B LEU* 3.3 11.2 + - + +
162B ALA* 3.9 21.8 - - + -
163B ILE 5.9 0.2 - - - +
164B LEU* 5.7 3.4 - - + -
171B LEU 6.0 0.7 - - - +
172B ARG* 5.6 6.3 - - - +
197B ILE* 3.9 10.8 - - + -
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Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ILE* 3.8 33.0 - - + -
131B LYS 3.5 2.2 - - - +
132B GLY 3.9 6.5 - - - +
133B GLY* 3.6 28.9 - - - +
139B PRO* 1.3 73.2 - - - +
141B LEU* 1.3 58.1 + - - +
162B ALA* 3.1 6.2 - - - +
163B ILE* 2.8 54.3 + - + +
171B LEU* 4.2 20.6 + - + +
174B ALA* 4.4 3.4 - - + +
175B THR 4.0 5.6 - - - +
176B HIS* 4.1 7.2 - - - +
179B ALA* 3.6 28.5 - - + -
183B LEU* 5.1 0.4 - - + -
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A MET* 4.0 16.2 - - + -
130B ILE* 3.1 7.8 - - - -
131B LYS* 2.8 57.7 + - + +
138B MET* 3.4 31.0 - - + -
139B PRO* 3.7 10.5 - - + +
140B ILE* 1.3 73.2 - - - +
142B ILE* 1.3 66.3 + - - +
160B GLY* 3.9 18.4 - - - +
161B ASP 3.3 4.7 - - - +
162B ALA* 4.0 6.7 - - + -
163B ILE* 5.3 0.2 - - - -
197B ILE* 3.6 32.3 - - + -
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Residues in contact with ILE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ILE* 3.8 24.5 - - + -
129B SER 3.6 4.9 - - - +
130B ILE* 4.5 0.4 - - - -
131B LYS* 4.7 2.6 + - - -
141B LEU* 1.3 71.8 - - - +
143B SER* 1.3 58.9 + - - +
144B LYS 3.7 21.1 - - - +
145B ILE* 3.8 19.1 - - + -
157B LEU* 3.9 39.7 - - + -
158B ARG 3.8 14.4 - - - +
159B LEU* 3.8 4.3 - - + +
160B GLY* 3.0 25.8 + - - -
161B ASP* 2.8 30.0 + - + +
163B ILE* 4.0 17.0 - - + -
192B LEU* 5.6 0.4 - - + -
194B VAL* 5.0 0.4 - - + -
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ASN* 2.5 30.3 + - - -
129B SER* 2.7 32.1 + - - -
130B ILE 3.7 2.3 - - - -
131B LYS* 3.9 27.6 - - - +
141B LEU 3.4 0.8 + - - -
142B ILE* 1.3 71.7 - - - +
144B LYS* 1.3 58.7 + - - +
159B LEU* 3.4 16.2 - - - +
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Residues in contact with LYS 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ILE* 3.1 8.5 - - - +
129B SER* 2.8 40.9 + - - +
142B ILE* 3.7 1.7 - - - +
143B SER* 1.3 81.2 - - - +
145B ILE* 1.3 75.8 + - - +
146B PHE* 3.6 38.2 - - + +
147B PRO* 5.3 5.2 - - - -
159B LEU* 3.3 7.9 - - - +
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Residues in contact with ILE 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLY 3.9 2.7 - - - -
128B ILE* 4.3 5.4 - - + -
142B ILE* 3.8 14.8 - - + -
144B LYS* 1.3 81.3 - - - +
146B PHE* 1.3 63.8 + - - +
147B PRO* 3.4 9.0 - - - +
151B ALA* 4.3 6.7 - - + +
152B ASP* 3.7 43.7 - - + +
157B LEU* 3.5 40.2 - - + +
158B ARG* 3.7 15.5 - - - +
159B LEU* 3.7 11.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il